Problem with dyn.load in R 2.13.0
On 04/13/2011 11:34 AM, Dirk Eddelbuettel wrote:
On 13 April 2011 at 13:00, Terry Therneau wrote:
| I have a test directory for the survival suite, and dyn.load has ceased
| to work in it. Below shows the log:
|
| tmt1075% R --vanilla
|
| R version 2.12.2 (2011-02-25)
| Copyright (C) 2011 The R Foundation for Statistical Computing
| ISBN 3-900051-07-0
| Platform: x86_64-unknown-linux-gnu (64-bit)
[...]
|> dyn.load('survival.so')
|> q()
[...]
|
| tmt1076% R13 --vanilla
|
| R version 2.13.0 RC (2011-04-11 r55409)
| Copyright (C) 2011 The R Foundation for Statistical Computing
| ISBN 3-900051-07-0
| Platform: x86_64-unknown-linux-gnu (64-bit)
[...]
|> dyn.load('survival.so')
| Error in dyn.load("survival.so") :
| unable to load shared object
| '/people/biostat2/therneau/research/surv/Rtest/survival.so':
| libR.so: cannot open shared object file: No such file or directory
|> q()
|
| --------------------------
|
| Is the issue that the .so file must have been created with the R2.13
| script? That's not what the error message says, however. It almost
| looks like it is ignoring my first argument and looking instead for
| "libR".
What does 'ldd /path/to/your/survial.so' say? Does the system find libR.so?
Maybe R CMD ldd /path/to/your/survival.so to pick up whatever environment R configures. Martin
I have no issues whatsoever on my Ubuntu box with the packages distributed
via CRAN (and now also a PPA if you want alpha/beta/rc builds) based on the
underlying Debian package I maintain.
I have a (pretty visible) hourly cronjob that drives our littler /usr/bin/r
frontend to do the CRANberries summaries---and even while /usr/bin/r was last
built under R 2.11.1, it continued to work merrily under R 2.12.0, 2.12.1,
2.12.2, and 2.13.0 prereleases:
edd at max:~$ r --version | head -4
r ('littler') version 0.1.3
svn revision 178 as of 2010-01-05 20:57:41
built at 20:08:17 on Oct 11 2010
using GNU R Version 2.11.1 (2010-05-31)
edd at max:~$
edd at max:~$ R --version | head -1
R version 2.13.0 RC (2011-04-07 r55373)
edd at max:~$
Both use the same shared library version libR.so from whichever current
r-base-core is installed.
So I see no particular breakage. Recompiling your project may also be a start.
Hth, Dirk
Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793